dchaley / deepcell-imaging

Tools & guidance to scale DeepCell imaging on Google Cloud Batch
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Get batch configuration fields from config file #286

Closed dchaley closed 3 months ago

dchaley commented 3 months ago

This adds a --configuration flag to the job launchers, which refers to a JSON file that we merge into the base job parameters. The config overrides whatever the base job says.

Use this to specify a network, subnetwork, service account, etc.

Paired with @WeihaoGe1009

Fixes #284

dchaley commented 3 months ago

Hi @bnovotny using this config approach, you can have a config file (see example-config.json) that specifies the fields you need. Then you'd just add --configuration=/path/to/your/config.json to the job launcher.

(Maybe we can put config in some well-known location to load automatically……)

bnovotny commented 3 months ago

I just used this along with run-qupath-job.py and everything looks good! The only tricky part for me is remembering all the arguments 😅 Thank you so much @dchaley and @WeihaoGe1009!!